The methodology of multi-scale structural assessment of the different cellulose fibre cement boards subjected to high temperature treatment was proposed. Two specimens were investigated: Board A (air-dry reference specimen) and Board B (exposed to a temperature of 230 °C for 3 h). At macroscale all considered samples were subjected to the three-point bending test. Next, two methodologically different microscopic techniques were used to identify evolution (caused by temperature treatment) of geometrical and mechanical morphology of boards. For that purpose, SEM imaging with EDS analysis and nanoindentation tests were utilized. High temperature was found to have a degrading effect on the fibres contained in the boards. Most of the fibres in the board were burnt-out, or melted into the matrix, leaving cavities and grooves which were visible in all of the tested boards. Nanoindentation tests revealed significant changes of mechanical properties caused by high temperature treatment: “global” decrease of the stiffness (characterized by nanoindentation modulus) and “local” decrease of hardness. The results observed at microscale are in a very good agreement with macroscale behaviour of considered composite. It was shown that it is not sufficient to determine the degree of degradation of fibre-cement boards solely on the basis of bending strength; advanced, microscale laboratory techniques can reveal intrinsic structural changes.